Everything we know about Jon Snow's mysterious true father on 'Game of Thrones'

Warning: Spoilers ahead for "Game of Thrones," including speculation of future events.

Two of the most important figures in the "Game of Thrones" universe — Rhaegar Targaryen and Lyanna Stark — are also the most mysterious and unexplored characters on the series. While show-only fans have heard the name Rhaegar intermittently, they might not understand the deep importance he has in the show's fictional universe.

Prince Rhaegar's early years and the Mad King

Rhaegar was the first-born child of King Aerys II (who was married to his sister, Rhaella). In the "A Song of Ice and Fire" books, Barristan Selmy tells Daenerys Rhaegar was "bookish" as a child and not interested in fighting:

"As a young boy, the Prince of Dragonstone was bookish to a fault. He was reading so early that men said Queen Rhaella must have swallowed some books and a candle whilst he was in her womb. Rhaegar took no interest in the play of other children.

The maesters were awed by his wits, but his father's knights would jest sourly that Baelor the Blessed had been born again. Until one day Prince Rhaegar found something in his scrolls that changed him. No one knows what it might have been, only that the boy suddenly appeared early one morning in the yard as the knights were donning their steel. He walked up to Ser Willem Darry, the master-at-arms, and said, 'I will require sword and armor. It seems I must be a warrior.'"

Some fans believe Rhaegar read about a prophecy in those scrolls — a prophecy which motivated most of his life choices from then on. But more on that later.

By the time he was 17, Prince Rhaegar was already knighted and winning tournaments, beating legendary warriors like Barristan Selmy. He often played the harp and sang beautifully at feasts and gatherings, and noblewomen around Westeros swooned over his silver hair and dark indigo eyes.

In the books, Cersei remembers her excitement when she believed her and Rhaegar would marry one day. "Next to Rhaegar, even her beautiful Jaime had seemed no more than a callow boy," Martin wrote.

Meanwhile, his father King Aerys grew more paranoid and resentful by the day.

During a small rebellion in which a rebelling lord held King Aerys hostage, Tywin Lannister (who was Hand of the King) seemed unconcerned about his potential death, saying, "We have a better king right here," as he gestured towards Rhaegar.

Once the rebellion was ended, King Aerys was more paranoid than ever. He believed Rhaegar and Tywin had plotted together to have him slain, "opening the way for Rhaegar to mount the Iron Throne and marry Lord Tywin's daughter."

King Aerys refused Tywin's offer of marrying Rhaegar to Cersei Lannister. Instead, Rhaegar was married to Princess Elia Martell of Dorne, the younger sister to Oberyn and Doran Martell. They had two children together, Rhaenys and Aegon.

Rhaegar and Elia chose to live on Dragonstone instead of in King's Landing. which only fueled Aerys' suspicions that Rhaegar was plotting against him and wanted the Iron Throne for himself.

The fateful Tourney of Harrenhal

In "A World of Ice and Fire," the story of the tournament in Harrenhal begins ominously:

"Many tales have grown up around Lord Whent's tournament: tales of plots and conspiracies, betrayals and rebellions, infidelities and assignations, secrets and mysteries, almost all of it conjecture. The truth is known to only a few, some of whom have long passed beyond this mortal vale and must forever hold their tongues."

One such rumor is that the tournament was secretly funded and organized by Prince Rhaegar himself, who was using Lord Whent as a decoy. People believed the tournament was a way to cover up the mass gathering of every important lord "in order to discuss ways and means of dealing with the madness of his father, possibly by means of a regency or a forced abdication."

At the tournament, Rhaegar and Lyanna Stark — Jon's mother — met for the first time. Here we must turn to a story about the tournament and a mysterious knight told by Meera and Jojen read in "A Song of Ice and Fire."

The story is about Howland Reed, Meera and Jojen's father, and how he was attacked by three squires at the Tourney of Harrenhal. Lyanna Stark intervened and brought Howland back to her tent to three Stark boys —Benjen, Ned, and Brandon.

The Starks convinced Howland to stay and enjoy the festivities. In the tale, we hear how Howland watched as Rhaegar Targaryen sang a song during one of the tournament feasts. The ballad was so beautiful it made Lyanna cry and her brothers teased her.

The next day, a mysterious person entered the tournament wearing ill-fitted armor and bearing a shield with a laughing weirwood tree painted on it. The Knight of the Laughing Tree challenged the three squires who had attacked Howland and won.

A popular theory among fans is that this knight was actually Lyanna. She was known for her prodigious horse-riding skills (a must for anyone jousting) and would have needed to disguise her appearance since she's a woman.

But the Mad King Aerys was furious when he saw the Knight of the Laughing Tree's victory, because he believed it was one of his enemies making a mockery of him. When the mystery knight seemed to vanish overnight, King Aerys sent Rhaegar to look for him.

Allegedly Rhaegar only found the knight's shield — but what if he really found Lyanna and chose to protect her from his father? Was this the beginning of their fated relationship?

The "kidnapping" of Lyanna Stark

Prince Rhaegar eventually won the tournament and was given a crown of blue winter roses so he could name the "Queen of Love and Beauty." Instead of choosing his wife Elia (who was there) Rhaegar gave the winter roses to Lyanna Stark (who was already betrothed to Robert Baratheon).

"When Rhaegar won, everyone cheered for their prince. I remember the guards laughing when he took off his helmet and they saw that silver hair and how handsome he was. Until he rode right past his wife, Elia Martell, and all the smiles died. I've never seen so many people so quiet. He rode past his wife and he lay a crown of winter roses in Lyanna's lap — blue with frost. How many tens of thousands had to die because Rhaegar chose your aunt?"

Littlefinger spoke with Sansa in the crypts of Winterfell on season five. HBO

According to "A World of Ice and Fire," Lyanna's brothers were furious at Rhaegar's decision and considered it a slight against Lyanna's honor as a noblewoman.

Some months later, after the tournament, Rhaegar and a dozen of his closest companions journeyed out into the Riverlands where he met Lyanna once again.

"Not ten leagues from Harrenhall, Rhaegar fell upon Lyanna Stark of Winterfell and carried her off, lighting a fire that would consume his house and kind and all those he loved — and half the realm besides," Martin wrote in "A World of Ice and Fire."

While some Westerosi called it a "kidnapping," we really don't know any details about how Rhaegar and Lyanna happened to meet that day, nor why they disappeared together. Could they have planned the meeting? Was it happenstance?

The Tower of Joy and Rhaegar's death

After the "kidnapping," Lyanna's father Rickard and oldest brother Brandon went to King's Landing to demand Aerys address Rhaegar's "crime." Aerys murdered Brandon and Rickard, and then ordered the execution of Ned Stark and Robert Baratheon.

Robert — who was furious over the disappearance of his betrothed and believed Rhaegar had stolen her and raped her — led the rebellion against King Aerys and his son.

As the war waged in Westeros, no one knew for certain where Lyanna was being held while Rhaegar led the Targaryen forces in battle. Elia Martell and her children were kept in King's Landing — King Aerys wanted them close.

Robert Baratheon waged war to avenge the atrocities committed against Lyanna and Ned's family. HBO

The fight came to head at the Trident river, where Prince Rhaegar Targaryen and Robert Baratheon fought fiercely in one-on-one combat. Robert crushed in Rhaegar's chest with his warhammer, scattering the rubies from his Targaryen armor into the river.

In the books, Daenerys has a series of visions from the House of the Undying. One of these visions was her brother Rhaegar's death: "Rubies flew like drops of blood from the chest of a dying prince, and he sank to his knees in the water and with his last breath murmured a woman's name."

That woman's name was likely Lyanna Stark.

After the rebellion was won, Ned went looking for his sister and found her in Dorne at a place referred to as the Tower of Joy. On the sixth season of "Game of Thrones," Bran had a vision of Ned's arrival to the tower. He and Howland Reed killed the kingsguard stationed there, and Ned went into the tower only to find Lyanna dying. In Ned's memories, she was clutching withering blue rose petals and laying in a bed of blood.

Ned and Lyanna in the Tower of Joy on season six. HBO

She had given birth to a baby boy — Jon Snow — and begged Ned to take her son and protect him from Robert's wrath.

Jon Snow and the Prince That Was Promised prophecy

As mentioned earlier, Rhaegar seemed to change after reading a set of scrolls. In the books, Aemon Targaryen (the maester of Castle Black and brother to the Mad King Aerys), tells Sam Tarly that he and Rhaegar discussed a prophecy known as the Prince That Was Promised.

At first, both Aemon and the Dragon Prince believed Rhaegar himself was the prophesied hero. "Later he became persuaded that it was his own son who fulfilled the prophecy," Aemon says in the books.

Aemon Targaryen and Sam Tarly on "Game of Thrones." Helen Sloan/HBO

Another of Daenerys' House of the Undying visions was of Rhaegar, and a woman who was likely Elia Martell with his newborn son Aegon.

"Will you make a song for him?" the woman asked.

"He has a song," the man replied. "He is the prince that was promised, and his is the song of ice and fire." He looked up when he said it and his eyes met Dany's, and it seemed as if he saw her standing there beyond the door. "There must be one more," he said, though whether he was speaking to her or the woman in the bed she could not say. "The dragon has three heads."

He went to the window seat, picked up a harp, and ran his fingers lightly over its silvery strings. Sweet sadness filled the room as man and wife and babe faded like the morning mist, only the music lingering behind to speed her on her way.

Rhaegar had two children with Elia, and it's possible that his "the dragon has three heads" line meant he believed he needed three children in order to fulfill the prophecy. Some believe Elia was too weakened after having two children, and was unable to carry a viable pregnancy for a third time.

This might tie into Rhaegar's relationship with Lyanna and his possible obsession with the Prince That Was Promised prophecy, especially if he legally cast aside Elia in order to marry Lyanna and have a third legitimate child.

Jon Snow is not the bastard he believes he is. Helen Sloan/HBO

If Jon was born from a legitimate marriage between Rhaegar and Lyanna, that makes him Prince Jon Targaryen. Coupled with Lyanna's oft-quoted last words to Ned, "promise me," Jon is literally the Prince That Was Promised.

There's still so much we don't know

Rhaegar's actions bring so many questions to the surface. Did he truly love Lyanna, or was she a tool through which he wanted to bring a prophecy to life? Why did he cast aside Elia, and how much did she know about his relationship with Lyanna? Did Rhaegar realize he was sentencing the Seven Kingdoms to decades of war and strife when he chose Lyanna? And lastly, will Jon Snow ever learn about his true lineage and possible claim to the Iron Throne?

"Game of Thrones" has yet to show Prince Rhaegar, even in a flashback. And while the slow drip of information is keeping fans on their toes, we hope to learn more about this mysterious character in the future.